The response to antigen, virus, or mRNA vaccine uptake was compared across samples, the general approach:
Project 3 will use LYTACs and EndoTags to direct antigen into specific endocytic compartments. Expression of relevant receptors is shown below.
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## time zone: America/Denver
## tzcode source: system (glibc)
##
## attached base packages:
## [1] tools stats4 grid stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] sp_2.1-0 sf_1.0-16
## [3] SpatialOmicsOverlay_1.0.0 umap_0.2.10.0
## [5] GeoMxWorkflows_1.6.0 GeomxTools_3.4.0
## [7] NanoStringNCTools_1.8.0 cli_3.6.1
## [9] devtools_2.4.5 usethis_2.2.2
## [11] here_1.0.1 broom_1.0.5
## [13] knitr_1.44 lubridate_1.9.3
## [15] forcats_1.0.0 stringr_1.5.0
## [17] dplyr_1.1.3 purrr_1.0.2
## [19] readr_2.1.4 tidyr_1.3.0
## [21] tibble_3.2.1 tidyverse_2.0.0
## [23] pzfx_0.3.0 png_0.1-8
## [25] xlsx_0.6.5 openxlsx_4.2.5.2
## [27] qs_0.25.5 ggtree_3.8.2
## [29] MetBrewer_0.2.0 ggVennDiagram_1.5.2
## [31] ggtrace_0.2.0.9000 ggtext_0.1.2
## [33] patchwork_1.2.0 colorblindr_0.1.0
## [35] colorspace_2.1-0 RColorBrewer_1.1-3
## [37] ggrepel_0.9.3 cowplot_1.1.1
## [39] ggbeeswarm_0.7.2 ggforce_0.4.1
## [41] scales_1.3.0 ggspruce_0.1.0
## [43] caret_6.0-94 lattice_0.21-8
## [45] ggplot2_3.5.1 furrr_0.3.1
## [47] future_1.33.0 ranger_0.15.1
## [49] rsample_1.2.0 gtools_3.9.4
## [51] boot_1.3-28.1 mixtools_2.0.0
## [53] GOSemSim_2.26.1 org.Mm.eg.db_3.17.0
## [55] AnnotationDbi_1.62.2 IRanges_2.34.1
## [57] S4Vectors_0.38.2 Biobase_2.60.0
## [59] BiocGenerics_0.46.0 msigdbr_7.5.1
## [61] enrichplot_1.20.3 clusterProfiler_4.8.3
## [63] biomaRt_2.56.1 gprofiler2_0.2.2
## [65] hdf5r_1.3.11 M3Drop_1.26.0
## [67] numDeriv_2016.8-1.1 djvdj_0.1.0
## [69] harmony_1.1.0 presto_1.0.0
## [71] data.table_1.14.8 Rcpp_1.0.11
## [73] clustifyrdata_1.1.0 clustifyr_1.12.0
## [75] SeuratObject_4.1.4 Seurat_4.4.0
## [77] ComplexHeatmap_2.16.0 meta_8.0-1
## [79] metadat_1.2-0
##
## loaded via a namespace (and not attached):
## [1] igraph_1.5.1 ica_1.0-3
## [3] plotly_4.10.2 Formula_1.2-5
## [5] zlibbioc_1.46.0 tidyselect_1.2.0
## [7] bit_4.0.5 doParallel_1.0.17
## [9] clue_0.3-65 rjson_0.2.21
## [11] urlchecker_1.0.1 blob_1.2.4
## [13] S4Arrays_1.0.6 parallel_4.3.1
## [15] plotrix_3.8-4 ggplotify_0.1.2
## [17] outliers_0.15 askpass_1.2.0
## [19] openssl_2.1.1 goftest_1.2-3
## [21] GenSA_1.1.14 kernlab_0.9-32
## [23] densEstBayes_1.0-2.2 uwot_0.1.16
## [25] shadowtext_0.1.2 curl_5.1.0
## [27] mime_0.12 evaluate_0.22
## [29] tidytree_0.4.5 tiff_0.1-12
## [31] leiden_0.4.3 stringi_1.7.12
## [33] pROC_1.18.5 backports_1.4.1
## [35] lmerTest_3.1-3 XML_3.99-0.14
## [37] httpuv_1.6.11 magrittr_2.0.3
## [39] rappdirs_0.3.3 splines_4.3.1
## [41] prodlim_2023.08.28 RApiSerialize_0.1.2
## [43] jpeg_0.1-10 ggraph_2.1.0
## [45] sctransform_0.4.1 sessioninfo_1.2.2
## [47] DBI_1.1.3 jquerylib_0.1.4
## [49] withr_2.5.1 systemfonts_1.0.4
## [51] class_7.3-22 rprojroot_2.0.3
## [53] lmtest_0.9-40 bdsmatrix_1.3-6
## [55] tidygraph_1.2.3 BiocManager_1.30.22
## [57] htmlwidgets_1.6.2 fs_1.6.3
## [59] SingleCellExperiment_1.22.0 segmented_1.6-4
## [61] labeling_0.4.3 cellranger_1.1.0
## [63] MatrixGenerics_1.12.3 reticulate_1.38.0
## [65] zoo_1.8-12 GGally_2.2.0
## [67] XVector_0.40.0 timechange_0.2.0
## [69] foreach_1.5.2 fansi_1.0.5
## [71] caTools_1.18.2 timeDate_4022.108
## [73] ggiraph_0.8.7 RSpectra_0.16-1
## [75] irlba_2.3.5.1 gridGraphics_0.5-1
## [77] ellipsis_0.3.2 lazyeval_0.2.2
## [79] yaml_2.3.7 survival_3.5-5
## [81] scattermore_1.2 crayon_1.5.2
## [83] RcppAnnoy_0.0.21 progressr_0.14.0
## [85] tweenr_2.0.2 later_1.3.1
## [87] profvis_0.3.8 ggridges_0.5.4
## [89] codetools_0.2-19 base64enc_0.1-3
## [91] GlobalOptions_0.1.2 KEGGREST_1.40.1
## [93] bbmle_1.0.25 Rtsne_0.16
## [95] shape_1.4.6 filelock_1.0.2
## [97] foreign_0.8-84 pkgconfig_2.0.3
## [99] xml2_1.3.5 mathjaxr_1.6-0
## [101] EnvStats_2.8.1 GenomicRanges_1.52.1
## [103] aplot_0.2.2 spatstat.sparse_3.0-2
## [105] ape_5.7-1 viridisLite_0.4.2
## [107] xtable_1.8-4 plyr_1.8.9
## [109] httr_1.4.7 globals_0.16.2
## [111] hardhat_1.3.0 pkgbuild_1.4.2
## [113] beeswarm_0.4.0 htmlTable_2.4.2
## [115] checkmate_2.3.0 nlme_3.1-162
## [117] loo_2.6.0 HDO.db_0.99.1
## [119] dbplyr_2.3.4 lme4_1.1-35.1
## [121] digest_0.6.33 Matrix_1.6-1.1
## [123] farver_2.1.2 tzdb_0.4.0
## [125] reshape2_1.4.4 ModelMetrics_1.2.2.2
## [127] yulab.utils_0.1.0 viridis_0.6.4
## [129] rpart_4.1.19 glue_1.6.2
## [131] cachem_1.0.8 BiocFileCache_2.8.0
## [133] polyclip_1.10-6 Hmisc_5.1-1
## [135] generics_0.1.3 Biostrings_2.68.1
## [137] classInt_0.4-10 CompQuadForm_1.4.3
## [139] mvtnorm_1.2-3 parallelly_1.36.0
## [141] pkgload_1.3.3 statmod_1.5.0
## [143] minqa_1.2.6 pbapply_1.7-2
## [145] SummarizedExperiment_1.30.2 vroom_1.6.4
## [147] gson_0.1.0 utf8_1.2.3
## [149] gower_1.0.1 graphlayouts_1.0.2
## [151] StanHeaders_2.26.28 readxl_1.4.3
## [153] gridExtra_2.3 shiny_1.7.5
## [155] lava_1.7.3 GenomeInfoDbData_1.2.10
## [157] RCurl_1.98-1.12 memoise_2.0.1
## [159] rmarkdown_2.25 pheatmap_1.0.12
## [161] downloader_0.4 RANN_2.6.1
## [163] stringfish_0.15.8 spatstat.data_3.0-1
## [165] rstudioapi_0.15.0 cluster_2.1.4
## [167] QuickJSR_1.0.7 rstantools_2.3.1.1
## [169] spatstat.utils_3.0-3 hms_1.1.3
## [171] fitdistrplus_1.1-11 munsell_0.5.0
## [173] rlang_1.1.1 GenomeInfoDb_1.36.4
## [175] ipred_0.9-14 circlize_0.4.15
## [177] mgcv_1.8-42 xfun_0.48
## [179] e1071_1.7-13 metafor_4.6-0
## [181] remotes_2.4.2.1 recipes_1.0.8
## [183] iterators_1.0.14 matrixStats_1.0.0
## [185] reldist_1.7-2 abind_1.4-5
## [187] rstan_2.32.3 treeio_1.24.3
## [189] rJava_1.0-6 fftwtools_0.9-11
## [191] bitops_1.0-7 ps_1.7.5
## [193] promises_1.2.1 inline_0.3.19
## [195] scatterpie_0.2.1 RSQLite_2.3.1
## [197] qvalue_2.32.0 proxy_0.4-27
## [199] fgsea_1.26.0 DelayedArray_0.26.7
## [201] GO.db_3.17.0 compiler_4.3.1
## [203] RBioFormats_1.0.0 prettyunits_1.2.0
## [205] listenv_0.9.0 tensor_1.5
## [207] units_0.8-5 MASS_7.3-60
## [209] progress_1.2.2 uuid_1.1-1
## [211] BiocParallel_1.34.2 gridtext_0.1.5
## [213] EBImage_4.42.0 babelgene_22.9
## [215] spatstat.random_3.1-6 R6_2.5.1
## [217] fastmap_1.1.1 fastmatch_1.1-4
## [219] vipor_0.4.5 ROCR_1.0-11
## [221] ggstats_0.5.1 nnet_7.3-19
## [223] gtable_0.3.4 KernSmooth_2.23-21
## [225] miniUI_0.1.1.1 deldir_1.0-9
## [227] ggthemes_5.0.0 htmltools_0.5.6.1
## [229] RcppParallel_5.1.7 bit64_4.0.5
## [231] spatstat.explore_3.2-3 lifecycle_1.0.3
## [233] zip_2.3.0 processx_3.8.2
## [235] nloptr_2.0.3 callr_3.7.3
## [237] xlsxjars_0.6.1 sass_0.4.7
## [239] vctrs_0.6.3 spatstat.geom_3.2-5
## [241] DOSE_3.26.2 ggfun_0.1.3
## [243] future.apply_1.11.0 entropy_1.3.1
## [245] bslib_0.5.1 pillar_1.9.0
## [247] magick_2.8.2 gplots_3.1.3
## [249] locfit_1.5-9.8 BiocStyle_2.28.1
## [251] jsonlite_1.8.7 GetoptLong_1.0.5